freefoam-setsToZones — Add pointZones/faceZones/cellZones to the mesh from similar named pointSets/faceSets/cellSets.
freefoam setsToZones [-help] [-noFlipMap] [-latestTime] [-noZero] [-srcDoc] [-doc] [-time <time>] [-constant] [-parallel] [-case <dir>]
There is one catch: for faceZones you also need to specify a flip condition which basically denotes the side of the face. In this app it reads a cellSet (xxxCells if xxx is the name of the faceSet) which is the masterCells of the zone. There are lots of situations in which this will go wrong but it is the best I can think of for now.
If one is not interested in sideNess specify the -noFlipMap command line option.